SMTL ID : 7rai.1

Cryo-EM structure of M4008_N1 Fab in complex with BG505 DS-SOSIP.664 Env trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 4 residues within 4Å: Chain A: V.104, T.105, N.118 Chain D: N.53 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.53, D:N.53 NAG-NAG-BMA-MAN-MAN.13: 4 residues within 4Å: Chain E: V.104, T.105, N.118 Chain H: N.53 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:N.53, H:N.53 NAG-NAG-BMA-MAN-MAN.25: 4 residues within 4Å: Chain I: V.104, T.105, N.118 Chain L: N.53 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:N.53, L:N.53

15 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 6 residues within 4Å: Chain A: T.98, Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain A: N.332, S.333, S.334, S.357 Ligands: NAG-NAG.10, NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.9, NAG-NAG.9, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG-NAG.10, NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain A: N.232, L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain E: T.98, Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain E: N.332, S.333, S.357 Ligands: NAG-NAG.22, NAG-NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.21, NAG-NAG.21, NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: S.357, N.361 Ligands: NAG-NAG.22, NAG-NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 6 residues within 4Å: Chain E: N.232, L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.16 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 6 residues within 4Å: Chain I: T.98, Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain I: N.332, S.333, S.357 Ligands: NAG-NAG.34, NAG-NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG-NAG.33, NAG-NAG.33, NAG-NAG.35 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 4 residues within 4Å: Chain I: S.357, N.361 Ligands: NAG-NAG.34, NAG-NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 6 residues within 4Å: Chain I: N.232, L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.28 No protein-ligand interaction detected (PLIP)

15 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 7 residues within 4Å: Chain A: V.144, R.162, N.167 Chain I: R.278 Chain K: S.25, G.26, F.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 7 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, R.412, V.414 Ligands: NAG-NAG-BMA.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 8 residues within 4Å: Chain A: N.271, I.292, Q.408 Chain D: D.1, Q.27, Y.92, D.93, S.94 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.94 NAG-NAG-BMA.8: 7 residues within 4Å: Chain A: T.267, H.299, N.301, S.381, T.383, R.412 Ligands: NAG-NAG-BMA.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 7 residues within 4Å: Chain A: R.278 Chain C: S.25, G.26, F.28 Chain E: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 7 residues within 4Å: Chain E: Q.263, N.265, N.301, S.303, R.412, V.414 Ligands: NAG-NAG-BMA.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 8 residues within 4Å: Chain E: N.271, I.292, Q.408 Chain H: D.1, Q.27, Y.92, D.93, S.94 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.94 NAG-NAG-BMA.20: 7 residues within 4Å: Chain E: T.267, H.299, N.301, S.381, T.383, R.412 Ligands: NAG-NAG-BMA.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 7 residues within 4Å: Chain E: R.278 Chain G: S.25, G.26, F.28 Chain I: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 3 residues within 4Å: Chain I: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 7 residues within 4Å: Chain I: Q.263, N.265, N.301, S.303, R.412, V.414 Ligands: NAG-NAG-BMA.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 8 residues within 4Å: Chain I: N.271, I.292, Q.408 Chain L: D.1, Q.27, Y.92, D.93, S.94 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:S.94 NAG-NAG-BMA.32: 7 residues within 4Å: Chain I: T.267, H.299, N.301, S.381, T.383, R.412 Ligands: NAG-NAG-BMA.30 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 20 residues within 4Å: Chain A: E.181, P.182, L.231, N.232, F.345, N.346, G.348, I.407, Q.408, G.409, V.410, I.411, R.412, C.413, V.414, S.415 Chain C: H.59 Chain D: S.94, R.95 Ligands: NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.16: 20 residues within 4Å: Chain E: E.181, P.182, L.231, N.232, F.345, N.346, G.348, I.407, Q.408, G.409, V.410, I.411, R.412, C.413, V.414, S.415 Chain G: H.59 Chain H: S.94, R.95 Ligands: NAG-NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.28: 20 residues within 4Å: Chain I: E.181, P.182, L.231, N.232, F.345, N.346, G.348, I.407, Q.408, G.409, V.410, I.411, R.412, C.413, V.414, S.415 Chain K: H.59 Chain L: S.94, R.95 Ligands: NAG-NAG.36 No protein-ligand interaction detected (PLIP)

21 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.37: 4 residues within 4Å: Chain A: E.57, N.58 Chain B: F.8, S.17 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.107 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: N.204, S.244 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain D: G.16, N.18, K.76 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain E: E.57, N.58 Chain F: F.8, S.17 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain E: N.103 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.107 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain E: N.204, S.244 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: N.308, W.364 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain H: G.16, N.18, K.76 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain I: E.57, N.58 Chain J: F.8, S.17 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain I: N.103 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain I: N.107 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain I: N.204, S.244 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain I: N.308, W.364 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain L: G.16, N.18, K.76 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, K.W. et al., A site of vulnerability at V3 crown defined by HIV-1 bNAb M4008_N1. Nat Commun (2021)

Release Date

2021-11-17

Peptides

Envelope glycoprotein gp160: AEI
HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41: BFJ
M4008_N1 Fab heavy chain: CGK
M4008_N1 Fab light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
E

B
B

F
D

J
F

C
H

G
I

K
J

D
L

H
M

L
N

Envelope glycoprotein gp160

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41

M4008_N1 Fab heavy chain

M4008_N1 Fab light chain

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